The issue described above has been corrected as of vSphere 4.1 U3
reference release notes:
VMware vSphere ESXi 4.1 Update 3 Release Notes
quote:
"
Esxtop fails while attempting a batch capture on a server with 128 CPUs
When you attempt a batch capture on a server with 128 logical CPUs, the esxtop fails. This happens due to the limited buffer size of the header. Increasing the buffer size of the header resolves this issue.
"
If you're at this release (or later) I'd suggest contacting support to have your issue triaged.